Cellular functioning requires the translation of mRNA into protein. Part of this process is the movement and processing of RNA from the nucleus to the cytoplasm. mRNAs in the cytoplasm are also transported to different regions within a cell where they are locally translated. Translation also occurs on ribosomes which are complexes of RNAs and proteins. The RNAs that are associated with ribosomes, as well as the mRNAs that are transported and translated, associate with proteins that facilitate the directed movement of RNAs to their proper functional place within cells. These RNA binding proteins, in association with other proteins and the cytoskeleton of the cell, are primary regulators of this movement.
RNA-binding proteins are crucial cellular integrators that are at the nexus of genetic and environmental interactions. RNA-binding proteins are responsible for the conversion of genetic DNA information into RNA (transcription), the maturation of the transcribed RNA (splicing and editing), the transport of RNA from the nucleus to the cytoplasm and transport of mRNA throughout the cytoplasm to ribosomal sites of translation. Indeed, RNA-binding proteins are responsible for regulation of the translation of RNAs. This regulation is referred to as translational control and is key in cellular regulation. Furthermore, all cellular RNAs bind to multiple RNA-binding proteins and each type of RNA-binding protein can bind to multiple mRNA species. Indeed, RNAs should be classified as functional groups not based upon the proteins that they encode (e.g. g-protein coupled receptor family) but rather by the RNA-binding proteins that they interact with since these proteins regulate the expression of the bound RNAs.
There are over 500 different RNA binding proteins within cells which are involved in modulation of various physiological functions. Characterization of RNA binding proteins has been difficult. Typically, RNA fragments are used to select RNA binding proteins from a protein lysate. Identification of RNAs associated with the RNA binding protein is also important to understand the function of the RNA binding protein and what RNAs may be affected by dysfunction of the RNA binding protein.
Determination of RNAs which bind to the RNA binding protein is usually done by screening a pool of mRNAs or mRNA fragments with an RNA binding protein to identify those RNAs which associate with the RNA binding protein. Once one RNA has been identified which associates with the RNA binding protein, nucleotide sequence similarity or predicted RNA structure is often utilized to predict what other RNAs might share these structural features and associate with the RNA binding protein. Typically, these studies utilize gel shift assays and ultraviolet light induced protein-RNA cross-linking assays. However, these assays suffer from a lack of sensitivity and specificity that often result in erroneous results.